RetrogeneDB ID: retro_eeur_387

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_279893:3860..4078(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: MAGOH
• Ensembl ID: ENSEEUG00000015908
• Aliases: None
• Description: mago-nashi homolog, proliferation-associated (Drosophila) [Source:HGNC Symbol;Acc:6815]

Sequence

>retro_eeur_387
GGAAAATTCCGGCCACAAGTTCCTGGAATTTGAGTTCCGGCCCGATGGGTAAATTGAGGAATGCCAACAACAGCAATTAT
AAGAATGATGTTATGATCAGAAAAGAGGTTTAAATACATAAAAGTGTAATGGAGGAAATGAAGAGAATAATTGATGACAG
TGAAATTAACCAAGAAGATGATGCTTTGTGGCCGCCTCCTGATTGAGTAGGCCAGCAG

Alignment

ORF - retro_eeur_387 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.78 %
• Parental protein coverage: 83.72 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GKF-GHEFLEFEFRPDG-KLRYANNSNYKNDVMIRKEAYVHKSVMEELKRIIDDSEITKEDDALWPPPDR
          GKF.GH.FLEFEFRPDG.KLR.ANNSNYKNDVMIRKE...HKSVMEE.KRIIDDSEI..EDDALWPPPD.
Retrocopy GKF>GHKFLEFEFRPDG>KLRNANNSNYKNDVMIRKEV*IHKSVMEEMKRIIDDSEINQEDDALWPPPD*

Parental  VGRQ
          VG.Q
Retrocopy VGQQ

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP017611_brain	0.00 RPM	1.13 RPM
SRP017611_kidney	0.00 RPM	6.00 RPM
SRP017611_liver	0.00 RPM	1.61 RPM

ChIP-Seq

Erinaceus europaeus was not studied using ChIP-Seq data.

EST

Erinaceus europaeus was not studied using EST data.

TSS

Erinaceus europaeus was not studied using FANTOM5 data.

Lab

retro_eeur_387 was not experimentally validated.

Homology

Retrocopy orthology:

Erinaceus europaeus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009587	1 retrocopy	retro_amel_853,
Erinaceus europaeus	ENSEEUG00000015908	6 retrocopies	retro_eeur_232, retro_eeur_275, retro_eeur_387 , retro_eeur_45, retro_eeur_463, retro_eeur_568,
Felis catus	ENSFCAG00000025232	2 retrocopies	retro_fcat_1246, retro_fcat_980,
Rattus norvegicus	ENSRNOG00000012778	1 retrocopy	retro_rnor_1168,
Sorex araneus	ENSSARG00000012081	2 retrocopies	retro_sara_142, retro_sara_150,
Sus scrofa	ENSSSCG00000003849	3 retrocopies	retro_sscr_1007, retro_sscr_706, retro_sscr_977,